Shah Mohammad Faruque (Bengali: শাহ মোহাম্মদ ফারুক; born c. 1956) is a professor and the dean of the School of Environment and Life Sciences at Independent University Bangladesh (IUB).

His areas of research interest include microbial genomics, bacteriophages, environmental microbiology, ecology, and evolution of bacterial pathogens, particularly those associated with waterborne and foodborne diseases.

Addressing the health problems of developing countries, Faruque has contributed significantly to the understanding of natural mechanisms associated with the emergence of bacterial pathogens.

In collaboration with John Mekalanos, Adele H. Lehman Professor of Microbiology, Harvard Medical School, Boston, Faruque has contributed extensively to the recent understanding of the epidemiology, transmissibility and ecology of Vibrio cholerae.

His team has also conducted cutting-edge research in CRISPR-Cas systems carried by bacterial viruses such as the JSF series of bacteriophages, isolated and characterized by them.

It is vital to generate more knowledge on the underlying diversity and functions of this system to fully realize the potential of technologies like CRISPR gene editing.

Currently Faruque and his team have been studying the role of quorum sensing and bacterial communication through molecular signals in the environmental biology and epidemiology of the cholera pathogen.